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<table width="100%"><tr><td>plotBins(LGS)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
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<h2>Plot z-scores of bins of markers</h2>


<h3>Description</h3>

<p>
<code>plotBins</code> merges <code><a href="plotLGS.html">plotLGS</a></code> and <code><a href="zbins.html">zbins</a></code> in that it calculates the z-score of groups of markers (bins) and plots the score to produce an equivalent of a genome scan. Like other plots of genome scans, <code>plotBins</code> can be useful to visually inspect the outcome of a LGS experiment.
</p>


<h3>Usage</h3>

<pre>
plotBins(lgs= NULL, bins= NULL, bandw= 30, shading= c("white", "lightyellow2"), sigv= c(-1.8, -2.5, 1.8, 2.5), ...)
</pre>


<h3>Arguments</h3>

<table summary="R argblock">
<tr valign="top"><td><code>lgs</code></td>
<td>
A vector of allele ratios or an object of class <code>LGS</code> (i.e. output of <code><a href="simLGS.html">simLGS</a></code>). </td></tr>
<tr valign="top"><td><code>bins</code></td>
<td>
A vector of the same length as <code>allRatio</code> specifying which markers should be grouped together. If the argument passed to <code>allRatio</code> is a <code><a href="simLGS.html">simLGS</a></code> list, <code>zbins</code> will search for the <code>simLGS$ChrMap$Bins</code> vector. </td></tr>
<tr valign="top"><td><code>bandw</code></td>
<td>
Width of the bands produced on the plot to distinguih adjacent bins. </td></tr>
<tr valign="top"><td><code>shading</code></td>
<td>
A pair of colours to use to shade bins. </td></tr>
<tr valign="top"><td><code>sigv</code></td>
<td>
Optional vector of significance thresholds to be plotted as horizontal lines </td></tr>
<tr valign="top"><td><code>...</code></td>
<td>
Further arguments to pass to <code><a onclick="findlink('graphics', 'plot.html')" style="text-decoration: underline; color: blue; cursor: hand">plot</a></code>. </td></tr>
</table>

<h3>Details</h3>

<p>
<code>plotBins</code> uses <code><a href="zbins.html">zbins</a></code> to calculate z-scores. As in <code><a href="zbins.html">zbins</a></code>, if a set of bins is provided both with <code>lgs</code> (as list of class <code>LGS</code> containing a <code>"Bins"</code> component) and as a argument to <code>bins</code>, this latter will have precedence.
</p>


<h3>Value</h3>

<p>
A plot of z-scores vs bins is produced.</p>

<h3>Author(s)</h3>

<p>
Dario Beraldi &lt;<a href="mailto:dario.beraldi@ed.ac.uk">dario.beraldi@ed.ac.uk</a>&gt;
</p>


<h3>See Also</h3>

<p>
<code><a href="zbins.html">zbins</a></code> to simply extract z-scores.
</p>


<h3>Examples</h3>

<pre>
data(pcMap)
lgs1&lt;- simLGS(offspring=100, scenario="GrowthAdvantage99", map=pcMap, gen.dist="phy")
# Plot allele ratios using plotLGS
plotLGS(lgs1)

# Plot z-score of bins in pcMap
plotBins(lgs1)
# Plot z-scores of chromosomes
plotBins(lgs1, bins=lgs1$ChrMap$Chr)
</pre>

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